<p>Microplastics (MPs) are widespread in marine sediments, and they have become an emerging global pollutant due to their potential threats to marine ecosystems. However, there is limited research on the distribution of MPs and meiofauna in estuarine sediments. MPs and meiofauna abundances were identified in sediments of 12 stations along the Van Uc estuary in rainy and dry seasons. The results showed that the rainy season had significantly lower number of MPs (4.34–5.93 item/g of dry weight) than those of the dry season (12.7–17.2 items/g of dry weight) (<i>p</i> &lt; 0.05, <i>t</i>-test). PET, PVC, and nylon were the common polymers found in the sediment samples. Pearson correlation analysis revealed that MPs in sediments of the Van Uc estuary had a positive correlation with the meiofauna abundance (<i>r</i> = 0.33, <i>p</i> &lt; 0.01). In contrast, a negative relationship was observed between organic matter and MPs (<i>r</i> = − 0.49, <i>p</i> &lt; 0.0001) and/or meiofauna abundances (<i>r</i> = − 0.59, <i>p</i> &lt; 0.0001). This study provides new insights into the ecological relevance of MP contamination and confirms that the meiofauna community may serve as seasonal biomarkers of MP contamination in estuarine sediments.</p>